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Unlike Les Collaborateurs, the Mole in Charge keeps those loyalties secret. He does not need to be the single mole in the organization, there may be many others at strategic locations within it. This gives the hero a big problem, because some members of the organization are what they are supposed to be, and others are villains who Look Just Like Everyone Else. By force, the hero goes paranoid at any given member of the organization, unable to know if he's one of the good or bad guys.

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This list contains spoilers. Read at your own risk.

Examples:

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Anime and Manga

Code Geass has probably the ultimate version of this when Lelouch becomes Emperor in the final act of season 2, all with the intent of making everyone hate him and the Britannia policies so much they will turn away from it once he's assassinated.

In Death Note, Light is suspected of being the mass murderer Kira, but manages to throw off suspicions enough that he's allowed to join the task force hunting Kira, partly so he can fully clear his name, partly so L can keep a close eye on him. Being The Chessmaster, he figures out a way to kill the people in charge and assume control of the task force without letting anyone else in the organization realize his involvement.

Vergo, a member of the Donquixote Pirates, infiltrates the marines and ends up becoming a Vice Admiral, the third highest rank in the organization, with a military base and hundreds of men under his direct control.

Stussy is the leader of a very popular red-light district and a major figure in the global underworld. She is also a high-ranking government agent who uses her power and influence in the underworld to make contact with other highly influential criminals and arrest them. Or assassinate them, depending on the circumstances.

"Napping" Kyoshiro is the top Yakuza in Wano Country, and one of Orochi's strongest soldiers. He's actually Denjiro, a member of the Akazaya Nine and loyal vassal to the late Kozuki Oden. His appearance was changed by his immense rage at failing Oden and his family.

Kishou Arima is the most famous Ghoul Investigator, in charge of handling the most dangerous targets and guarding the vital Main Office for the organization. His duties also include pursuing the One-Eyed Owl, and the legendary One-Eyed King. It's eventually revealed that he is the One-Eyed King, and has been the Owl's partner for more than a decade in a long-running plan to bring down the Government Conspiracy.

After the Washuu Clan are massacred, the late chairman's bastard son is named as the next leader of the CCG. Nimura Furuta is an insignificant investigator, but quickly proves himself as a natural-born leader and takes charge during a surge of brutal attacks by the Clowns. Of course, it helps that Furuta himself led the massacre, and the Clowns are carrying out the attacks on his orders. His experience as a Double Reverse Quadruple Agent makes him an excellent actor, playing the role of a talented rookie with no confidence in order to propel himself into leadership.

Comic Books

This seems to happen to S.H.I.E.L.D. depressingly often in Nick Fury stories. As well after Carol Danvers is forced to step down Post Ultimatum. Her replacement is someone who in the 616 is known as Mentallo.

This caused more than a bit of Fan Dumb as it was during the Bush presidency and the name the Red Skull was using at the time had the initials D.R. OK, admittedly that's a funny coincidence, but "Dell Rusk" is an anagram of "Red Skull", so what else should the writers have called him?

Furthermore, if "Dell Rusk" were a reference to a real life Cabinet member, it would probably be to Dean Rusk, who was Kennedy and Johnson's Secretary of State.

Runaways: Alex Wilder becomes the undisputed team leader, only for it to be revealed that he was working with the Pride the entire time.

Daredevil once found himself ostensibly running the evil ninja assassins called the Hand. They corrupted him to the point that a demon actually possessed him briefly.

In Superman & Batman: Generations, Batman ultimately ends up accepting Ra's Al Ghul's offer to become his heir, and turns his terrorist organization into a world-spanning anti-crime unit.

In Superman: World of New Krypton, General Zod is severely injured before he can unleash his plan to invade Earth. While he recovers, the supreme commander of New Krypton's military forces is ... Commander Kal-El. Kryptonian foreign policy suddenly becomes a lot more diplomatic; unfortunately, it's temporary.

For a long time, this was a running sub-plot of the Kree/Skrull war in the Silver Surfer comics; a Skrull (locked in the form of a Kree woman) had somehow risen to the very top of the hierarchy of the Kree Empire.

Block 109: Zytek was first recruited by the anti-Nazi Admiral Wilhelm Canaris before the war to infiltrate the Nazi Party. Zytek's decision to assassinate Hitler ended up creating an even worse war than he feared, but he was eventually able to ascend to leadership of the Third Reich so he could dismantle it from within.

In The Swarm of War, a lot of senior human military commanders (the most successful ones) are actually the Swarm's spies. Then, Alena, the disguised Queen of Blades, makes herself the human queen.

The War of the Masters: Fleet Admiral Jorel Quinn, the head of Starfleet, is an Undine infiltrator who replaced the real Quinn. (This was a somewhat common WMG for Star Trek Online before it was jossed in the mission "Surface Tension".) As such, he is in a position to do serious harm to the Federation, and does so repeatedly, starting with signing off on the plan to forcibly resettle Klingon-border colonies and keeping Admiral Menninger in charge of the local Starfleet forces long after he should have been sacked. His Dragon is Rear Admiral David Huntington, who is a human Masters cultist and recurring villain. There are various other Undine infiltrators in high positions as well.

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Film  Animated

In Frozen, Anna names Prince Hans regent while she goes off to look for Elsa. At this point, his status as a villain hasn't been revealed yet.

Film  Live-Action

Cambridge Spies and all other retellings of the story of Kim Philby and his colleagues, Communist agents who rose to the top ranks of MI-5.

The Departed: Frank Costello is an FBI informant. Though that was after he had built up his empire as a self-defense measure. A better example is Colin Sullivan, Frank's mole in the State Police, and the head of a special Task Force in charge of finding the mole in the State police.

In The League of Extraordinary Gentlemen, M brings the titular league together on the premise that he needs their help to bring down The Fantom, a renowned criminal mastermind. In reality, M is one of The Fantom's alter-egos, and his real reason for recruiting the league was to steal from the members who had superpowers (Mina Harker's vampire blood, a skin sample from the Invisible Man, and Jekyll'sSuper Serum), duplicate their effects to add to his arsenal, then kill off the entire league in one swift blow.

In Men in Black: International, it turns out that The Mole is actually High T, the leader of the UK branch who was actually infected by the Hive and neuralized H into thinking he defeated them.

In Mission: Impossible  Fallout, Ethan Hunt is aided by the CIA's top agent August Walker to hunt down the Apostles and the mysterious terrorist John Lark. It turns out that Walker is John Lark the entire time.

In My Favorite Martian, the man in charge of the organization hunting aliens is himself an alien stranded on Earth, apparently looking for a spaceship that can finally take him home.

Now You See Me: It turns out at the end that the mysterious "Fifth Horsemen" giving the main character their orders, was Dylan Rhodes, a.k.a. Dylan Shrike, the FBI agent who had been trying to capture them the entire movie.

Red Sparrow has a heroic example. The mole in SVR that everyone's been looking for is General Korchnoi, who turned to the Americans in hopes of saving Russia from its own leaders after SVR wouldn't let his beloved wife be treated in an American hospital, resulting in her death.

RoboCop (2014): Crime boss Antoine Vallon has both the lead DPD detectives investigating him, as well as the Detroit Chief of Police on his payroll.

In Salt, the ending strongly suggests that the President dies from his wounds, and the Vice President who ascends to succeed him is another Russian sleeper agent. There's also the fact that the CIA agent in charge of hunting down the sleepers is actually a sleeper himself.

In Smokin' Aces it's revealed that the leader of the mob is really an FBI agent who was burned by his handlers and had to become a criminal for real to survive, eventually rising up the ranks to the top position.

Star Wars: In the prequel trilogy, Senator Palpatine becomes Chancellor of the Republic and Darth Sidious is the mastermind behind the invasion of Naboo and the Separatist Crisis, which turns into the CloneWars. They're the same person, whose ultimate goal is the downfall of the Republic and destruction of the Jedi Order, to be replaced with his own Empire. This succeeds. It then evolves into the conflict of the Galactic Civil War in the original trilogy (Episodes IV-VI).

Literature

Authors:

Tinker, Tailor, Soldier, Spy does this, more or less. The Mole is nominally the number 2 member of the organization, but actually in control of it. It was inspired by the unearthing of the Cambridge Five, who included Kim Philby (see below).

The Spy Who Came In from the Cold does the same thing, in reverse. Although he technically isn't the topman in the Stasi, Mundt is the highest-ranking East German intelligence officer who appears in the story and it turns out that he'd been turned years prior to the events of the book.

The Honor Harrington books managed to avoid them for quite some time, but then the Mesans, with an entire multi-generational network of moles, appeared. The entire Havenite Legislaturalist class were Alpha lines.

Safehold: The highest-ranking members of the colony administration staff turned out to have no intention of following the original Operation Ark plan, instead setting up the Human Popsicle colonists to follow a religion they'd invented tailored towards preventing the re-emergence of any kind of advanced technology.

Works:

In the Arsène Lupin novel 813, the Head of the French Police, the best detective ever seen, the only man everyone trusts to be able to catch Gentleman Thief Lupin... turns out to be Lupin himself in disguise.

An odd variant occurs in Jack London's The Assassination Bureau, Ltd. when Winter Hall, having paid the Bureau to kill its own leader, is placed in charge of handling the Bureau's correspondence and finances — the things the leader would normally do — while said leader is on the run from his team. The members of the Bureau know Hall is out to destroy them, because he told them ... but they all have an overpowering sense of ethics, and so they respect his honesty and consider him a friend. And he considers them friends, and now wants to find a way to destroy the organization without harming the members.

As told in Horrible Histories, the story of Fernando Buschman, a Brazilian-German violinist who was executed during World War I in the Tower of London for spying. He, as well as a group of spies, were all sent to their deaths by their spymaster, a British mole serving in Germany's intelligence wing. The Germans' entire "infiltration" method was a signal for the British Intelligence to quickly identify them and get them captured.

In The Illuminatus! Trilogy, Hagbard Celine, leader of the Legion of Dynamic Discord, is also a Primus Illuminatus, as well as a high-ranking member of A.'.A.'.. Given his stated beliefs, the conflict of interest makes perfect sense.

Of course, he took the place in The Illuminati purely to screw them up after he realized that he couldn't guide them to a more constructive path. His true loyalties, if such thing exists, lie with the A.'.A.'.

Older Than Radio: Konrad Wallenrod by Adam Mickiewicz is a classic of Polish Romanticism, in which he postulated using deceit (as opposed to direct action) against the occupiers. The plot involves a Lithuanian who rises in ranks of The Teutonic Knights, and after many years leads their army to a total defeat.

Lensman: In Second Stage Lensman, Lensman Kinnison goes undercover into the enemy military and works his way up to become a military dictator, Tyrant of Thrale, to find out who The Man Behind the Man is and to sabotage an upcoming battle.

In The Leonard Regime, the mole also happens to be the second in command of the entire rebellion.

In The Man Who Was Thursday the protagonist discovers that the Council of Days, supposedly the supreme council of the British anarchist underground, is made up entirely of undercover police officers like himself.

Mediochre Q Seth Series: Dean Kiwi Mashuga of St Merlin's University is secretly the head of the Sapphire Smuggling Syndicate. When an SSS member is asked - while attached to a lie detector - whether anyone in the university works for the SSS, she is able to truthfully answer 'no', because technically, the SSS works for Kiwi.

In Robert A. Heinlein's novel The Moon Is a Harsh Mistress, Adam Selene, figurehead of the Rebellion against the Lunar Authority, is in actuality a virtual construct of the Authority's main computer, who has quietly attained both sentience and a sense of humor.

At the end of the President's Vampire novel Red, White and Blood, Vice President Lester Wyman, who has been the Mole for the Shadow Company throughout the series, gives himself a Klingon Promotion.

The Star Trek: Myriad Universes story A Gutted World imagines the Cardassians found the Bajoran wormhole and never left Bajor. They also found the Dominion with the Founders soon replacing key people across the galaxy as Changelings. They instigate a full on war between the Federation, Romulans and Klingons. It soon turns out changelings have replaced General Martok, Tal Shiar officer Koval and Gul Dukat, all to drag the war out longer and leave all sides weakened for when the Dominion invade. Starfleet is dubious when Kira and Odo tell them so Kira uses a device that causes a changeling to lose control of their form...and the Federation President transforms into a Founder.

Star Wars Legends: In the X-Wing Series novel Mercy Kill, the A-plot follows a team of Wraiths assembled under Face Loran at the behest of his boss, General Maddeus, head of Galactic Alliance Intelligence. Their job is to look into the head of the army, General Stavin Thaal, and see if he has any connection to the "Lecersen Conspiracy", a plot by hard-line loyalists to return power to the Empire. It transpires that not only is Thaal part of the conspiracy, but so is Maddeus. He was worried that evidence might link them to the other known conspirators, so he sent Face to find it and report back to him, allowing him to tip off Thaal before the Wraiths could catch him. Then, he would eliminate both Face and the leaks he had revealed. Face outmaneuvers him by arranging for two teams of Wraiths while reporting on the actions of a third, fictitious, team; when Maddeus tries to warn Thaal about the fake Wraiths, his cover is blown.

The Wingman pulp series by Mack Maloney begins when the United States Vice President, a Soviet mole, arranges for the assassination of the President and lowers the Star Wars missile shield, allowing the remnants of the USSR to nuke the United States in revenge for destroying them in World War III.

In Worm, the Undersiders inadvertently help Coil become this, as his civilian identity replaces the local PRT director, putting him in control of not only every supervillain but every superhero in the city.

This happens on Alias at least once every thirty seconds. Between the "real" nature of SD-6, the loyalties of Derevko, the actions of Sark and the constant flip-flopping of characters between the CIA and other organizations... heck, there are even situations where a mole infiltrates an organization, rises to the top, then stages the infiltration of the organization they were moling for in the first place!

Babylon 5: Sheridan is this twice over — hired by the Clark government to spite the Minbari because of their perception of him as a war criminal, but actually a highly placed member of La Résistance, sent to determine the B5 crew's loyalty or lack thereof to the increasingly fascist EarthGov.

Kim Wexler becomes an unintended example in the fourth season of Better Call Saul: Her client bank Mesa Verde tasked her with evicting a man from the planned site of a call center, but she came to sympathize with him, and so had her boyfriend Saul represent him legally. Kim actually tries to get off the case by pointing out the blatant conflict of interest, but the head of Mesa Verde insists she stay.

In Caprica, Gara Singh is chief agent in the Caprica Global Defense Department and leader of the Soldiers of the One monotheistic terrorists on Caprica.

In the Castle episodes "Pandora" and "Linchpin" the villain is the second-in-command agent of a CIA operation. Strike that it was really the number one in command and she framed him. It further turns out she was a KGB agent who infiltrated the CIA just as the USSR went under and was thus a double mole.

When the BAU team was called in by the CIA to find a mole in their ranks, the mole was the Deputy Director.

In "Amplification", the BAU is looking for someone who unleashed an anthrax attack onto a group of people in a park. The person who did it turns out to be a high-ranking researcher for a government anti-terrorism agency. He unleashed the attack because he wanted the American populace to take terrorism more seriously and to demonstrate vulnerabilities in his agency's methods.

Daredevil: In season 3, Special Agent in Charge Tammy Hattley, who oversees the FBI agents assigned to protecting Wilson Fisk, turns out to have been blackmailed into working for Fisk, as have most of the agents on the detail.

Scorpius from Farscape is in charge of the Peacekeeper's wormhole weaponization project while being a double agent for the Scarrans. Except, it turns out Scorpius isn't really working for the Scarrans. He just lets them think that he is for as long as he can, so that he can develop wormhole weapons with which to destroy them.

Played for laughs on Get Smart when all four members of a KAOS cell turn out to be moles from different agencies: the CIA, the FBI, Naval Intelligence and Scotland Yard. The only real KAOS agent had died years ago without being replaced.

Played with on Grimm. Nick's boss, Captain Renard, is initially portrayed as The Mole and quite possibly the Big Bad. However, we later discover that his loyalties are way more complex. He is the illegitimate son of the head of the Royal Families but is also one of the leaders of the Resistance, a group of Wesen who oppose the Royals.

In Highlander, the Watchers have a research division that's dedicated to finding Methos, the legendary first Immortal. The lead researcher is Methos, and guarantees that they never find him.

On Intelligence (2006), a seasons-spanning storyline involved the discovery of a CIA mole in the highest echelons of the Canadian Security Intelligence Service and its fallout.

The series finale of Intelligence (2014) revealed that Weatherly, the Director of Central Intelligence was a deep-cover Iranian mole.

Madam Secretary: It turns out in "The Ninth Circle" that CIA Director Munsey is part of a Renegade Splinter Faction trying for regime change in Iran to stop them from getting the bomb, rather than let Liz and President Dalton's peace talks run their course.

One NCIS: Los Angeles episode has the team trying to prevent a highly placed US mole inside the Iranian military from having his cover blown. At the end of the episode, they've managed to reinforce the cover of the general in question so well that he's been promoted to head of counterintelligence.

In Případy 1. oddělení, technician Strompf is kicked off the department when Maj. Kozak finds out that he's the bastard selling tips to TV. However, Strompf blackmailed Maj. Korejs (head of the department) who gives him great references, so the mole gets hired by Internal Affairs. He later tries to destroy some of his former colleagues out of spite and is put in charge to investigate Maj. Kozak who is suspected of getting around a warrant search.

Subverted in The Prisoner (1967) episode "Free For All". Number 6 is elected to the position of Number 2, technically putting him in charge of the Village, but it turns out to be a cruel trick to break his mind.

The Star Trek: Deep Space Nine episode "Inter Arma Enim Silent Leges" has this as a major twist that changes your perception of the events of the episode: Koval, the chairman of the Tal Shiar (the Romulan intelligence organization) and staunch opponent of the Federation-Romulan alliance against the Dominion turns out to have been a Federation agent all along. The entire thing was a plot to remove a less reliable Senator from power and lend additional force to Koval's turn to supporting the alliance.

In Supergirl (2015), the leader of the Department of Extranormal Operations, a US government Men In Black group, turns out to be an alien in disguise who killed and replaced the real guy. In fact, he's the DC TV universe version of the Martian Manhunter. Also the previous guy isn't really dead.. Subverted, since it's revealed that the original leader was a fanatical and malevolent xenophobe, while the infiltrator wants to change the agency to genuinely protect the Earth from evil aliens while acting as a benevolent immigration service for more moral ones.

One episode of Yes, Prime Minister revolved around the revelation that a former head of MI-5 had, during his time in office, been a Russian agent.

Professional Wrestling

After the formation of the nWo, The Giant (later The Big Show) quickly became the leader of WCW's makeshift resistance. That is, until he had a FaceHeel Turn and became a member of the nWo. Later, WCW's Executive Vice President, Eric Bischoff also joined the nWo, and revealed that he'd been working for them the entire time.

When the Aces andEights invaded TNA, Bully Ray went out of his way to get the trust of Hulk Hogan and, seemingly inadvertently, the love of his daughter Brooke Hogan, which resulted in the Hogan family essentially anointing him as The Hero for TNA against the Aces and Eights and giving him a fast track to a World Heavyweight Championship match. The thing with that, as they painfully found out the night of said title match, is Bully Ray is thePresident of the Aces & Eights.

Tabletop Games

A bit of Planescape lore tells how an Anarchist infiltrated the Harmonium so deeply and for so long that he ended up the head of the latter faction. The Anarchist then ordered the Harmonium to disband... which promptly lead to his being arrested and tried for treason, and revealed as The Mole. Depending on your perspective, either a tremendouslyChaotic Stupid move by a mole in a position of power making life more difficult for any moles who come after him, or a brilliant Paranoia Gambit to make the Harmonium forever wonder what damage he had done on the way up and hindering their ability to trust one another ever after.

Sam & Max give us a literal example, since the mole inside the toy mafia takes over the mafia... and is actually a mole.

In BioShock 2, Sofia Lamb put Stanley Poole in control of Dionysus Park, her sanctum. He was Andrew Ryan's spy all along.

You can do this in the game Seven Kingdoms 2: The Frythan Wars using your spy units. The spy looks like any ordinary unit to everyone but the owner and the enemy treats it like an ordinary unit, including for being promoted to general status and running a fort. And even for promotion to king if their king is killed and the spy is a general. Having a spy as a general allows you to take control of a fort and make it switch colors as well as some of the units in it, depending on loyalty or simply screw with enemy operations by conflicting orders. If the spy becomes king then you automatically defeat that enemy. Be warned though, the AI is good at using spies against you too.

Ace Attorney Investigations: Miles Edgeworth has a major one. The head of the Yatagarasu caseisthe Yatagarasu, or at least one member of the group. Hell, the original Yatagarasu was made up of the prosecutor, detective, and the defense attorney on the case. Considering there's no jury in the Ace Attorney world and the Judge is an idiot, you can't get much more in charge than that.

One of the key plot points of Dawn of War II: Chaos Rising. Towards the end of the game the Blood Ravens learn that their Chapter Leader is actually a follower of Chaos. The game ends with the Blood Ravens under the player's command going rogue and setting off to expose the traitor.

In Soldier of Fortune 2, the Obviously Evil second-in-command of the anti-terrorist organization is also the leader of the main terrorist organization. It turns out he actually founded the terrorist organization to drum up business when the end of the Cold War caused a drop in demand for anti-terrorist services.

In the 2005 remake of NARC, the chief of the N.A.R.C. anti-drug task force is also the leader of K.R.A.K., the main drug cartel. It turns out she founded N.A.R.C. specifically to eliminate all the other competing drug cartels.

Fallout: New Vegas: There's a spy planted by Caesar in the New California Republic at Camp McCarran who's radioing out information, and they're trying to root out who it is. It happens to be the officer in charge of the investigation.

In Fallout 4, it's eventually revealed that Mayor McDonough of Diamond City is actually a Synth infiltrator, with the real one having been killed and replaced long ago.

In Strife, the leader of The Resistance is actually one of the 5 main leaders of The Order. His actions vary between giving his men suicide missions designed to get them killed, and genuine strikes against the Order which are really power grabs in an attempt to gain dominance over the other 4 leaders.

In Call of Juarez: The Cartel, the Mendoza Cartel's high-ranking mole inside the U.S. government turns out to be Department of Justice Deputy Assistant Director Shane Dickson, the head of the special task force assembled specifically to deal with the Mendoza Cartel. In fact, the task force was designed to fail from the beginning, which explains why all 3 members work together so poorly and are so obviously corrupt and/or insane.

Albert Wesker, in charge of the S.T.A.R.S. sent to the mansion in the first Resident Evil is also working for the company that made all the zombies in the first place.

In Resident Evil: Revelations head of the Federal Bioterrorism Commission Morgan Lansdale is responsible for the monster outbreak on board the Zenobia so the world will be more afraid of bioterrorism and give the FBC more power. He is opposed by the head of Bioterrorism Security Assessment Alliance Clive R. O'Brian, who sent in Jill, Chris, Parker, and Jessica to the Zenobia with incredibly lacking intel in an elaborate plan to expose Lansdale, which, while well-meaning, was such a dangerous Gambit Roulette that he deserves a little bit of scorn.

National Security Advisor Derek Simmons is the one responsible for the president's assassination and the zombie outbreak in Tall Oaks in Resident Evil 6.

In Kingdoms of Amalur: Reckoning, the Big Bad of the House of Sorrows Faction questline is the faction's leader who is actually a Tuatha agent. He is even the one who recruits the Fateless One into the faction and successfully manipulates him/her into removing one of the few obstacles left to his plan to destroy the House of Sorrows and claim its powerful magic for the Tuatha.

In Romance Of The Three Kingdoms II, you can hide officers in enemy territory to lower the loyalty of his officers. If his ruler dies, one of his officers (a relative if possible, the highest Charm officer otherwise) becomes the new ruler — which means that your mole may become their new ruler (and, if he does, he will promptly stop being a mole.

In Sleeping Dogs, Wei Shen becomes a Red Pole in the Sun On Yee after Winston is killed. While he doesn't reach the top of the Sun On Yee overall, he's still this trope for the subsidiary Water Street Boys gang, making him one of the most powerful people in the Triad hierarchy, and if he had wanted to and found support, he could have moved to become Dragon Head. Ultimately however, he goes back to being a cop and the new Triad boss lets him walk away out of respect for eliminating her enemies.

The Federation storyline in Escape Velocity Nova features this (Only the Federation storyline, mind — despite the Rashomon-y tendencies of the game, certain things only make sense if Schrödinger's Gun is in effect here): Frandall, head of Rebellion intelligence and former head of Federation Intelligence, turns out to be the real head of the Bureau.

A comedic example in Pajama Sam 2. Carrot infiltrates World Wide Weather believing it to be economically oppressing employees. A puzzle solution requires that Sam needs Carrot to get himself on the Board of Directors, and Sam leaves Carrot to act in his stead. Carrot quickly becomes very popular by introducing seating for all the board members and then he starts implementing employee benefit programs. In the end, when Sam returns to see Carrot running the company by himself, Carrot explains that he thought management was top-heavy and downsized the entire board of directors except himself.

Middle-earth: Shadow of Mordor: THE WHOLE DAMN POINT. Your goal as a Ranger with Wraith powers is to build an army out of Sauron's forces through mind control, thereby causing an Enemy Civil War strong enough to take down Sauron himself. Bad News: his army numbers in the millions. Good News: Sauron uses a mind control hierarchy, so that mind-controlled warchiefs have limited mind control over their lieutenants, and the lieutenants have limited mind control over the grunts. You either need to dominate a lieutenant and kill his warchief, thus allowing your mole to be instantly promoted to warchief, or dominate the leader himself.

In Snatcher, the JUNKER chief Cunningham is revealed to be this when you discover his corpse in the morgue of Queen's Hospital. When he's exposed, he kills Harry and takes Mika hostage.

Subtle occurrence in Mass Effect 3, where the Illusive Man is leading Cerberus against both the Reapers and the Council whilst trying to gain control of the former, but ends up indoctrinated by the Reapers instead.

It's revealed the Batarian leadership had been indoctrinated by exposure to a Reaper carcass they'd found, thus when the Reapers invaded through Batarian space, the Hegemony collapsed without any resistence.

It's revealed in the True Mastermind Edition of Time Crisis 5 that Robert Baxter, the one leading the investigation on finding a traitor within the VSSE, is the traitor all along.

In The Legend of Heroes: Trails of Cold Steel II, Rufus Albarea, the chief of staff of the entire Noble Alliance, is actually trying to undermine the very same alliance for his real boss, Chancellor Giliath Osborne.

In The Feeble Files, The Dragon somehow manages to become the leader of the Resistance, and tricks everyone into getting themselves captured. It becomes Feeble's task to save them.

In the first Fossil Fighters game, the Police Are Useless when it comes to keeping the BB Bandits under control. Even when they catch any Bandits, the cells are usually empty.That's because the BB Bandits' leader is the chief of police, Bartholomew Bullwort. He has a teleporter in the police station that connects to the BB Base, preventing any Bandits from staying locked up for too long.

Webcomics

Yu Hansung and Augusgus from Tower of God are test directors of the regime of Jahad, supervising two of the most important floors of the Tower, yet in secret, they are working for the terrorist syndicate FUG and know how to use their positions to their advantage.

In an episode of Captain Planet Gaia gets body-switched with one of the bad guys, leaving one of them to run her organisation and Gaia to "run" the bad guy organisation (by tricking them into acting in eco-friendly ways).

In Codename: Kids Next Door, we discover in the last few episodes that Numbuh 274/Chad, who became a very high-ranking member of the Teen-Ninjas was a Fake Defector still loyal to the KND.

Heroic example in Gargoyles: Detective Matt Bluestone is an ally of the Manhattan gargoyle clan, and gets appointed to the NYPD Gargoyle task force sent out to capture them. It puts him in a position to keep the odds high that his gargoyle friends elude capture.

G.I. Joe Extreme ended at least one season with the villain Iron Klaw masquerading as the military official in charge of G.I. Joe itself.

Star Wars: The Clone Wars: In the Umbara arc from Season 4, Anakin is called away to a Jedi meeting in the middle of a battle. His unit is temporarily commanded by Master Krell, who has secretly fallen to the Dark Side. He intentionally gives his troops reckless orders that get them killed, and at one point even tricks two groups of clones into shooting at each other before he is found out. It should be noted that Krell has not yet linked up with the Sith. He's hoping to get Count Dooku's attention by sabotaging the operation on Umbara so that he will be picked as Dooku's apprentice. He doesn't know that Dooku himself is the apprentice to Darth Sidious, AKA Republic Chancellor Palpatine (see above).

Star Wars Rebels has this occur in season three with Agent Kallus as the new Fulcrum due to a HeelFace Turn. Their high rank in the empire's Lothal garrison, specifically as an intelligence agent, makes them a valuable ally. However, this was also the season Grand Admiral Thrawn was put in charge of the Lothal situation and Governor Pryce took more of a commanding role, limiting Fulcrum's abilities; making it closer to a "mole who would have been in charge if higher-ups hadn't gotten involved."

Steven Universe: Pink Diamond was publicly the ruler of Earth and the leader of Homeworld's forces against Rose Quartz. In reality, she was Rose Quartz, and started the rebellion against herself because the other Diamonds didn't get that she'd had a Heel Realization and were forcing her to complete the colony against her will. It does make certain strategic decisions in the war make more sense in hindsight.

Stretch Armstrong and the Flex Fighters. Malcolm Kane, Rook Unlimited's Head of Security and essentially Jonathan Rook's right-hand man is really Number One, the leader of the Tech Men who used his former identity to infiltrate Rook Unlimited and gain trust and power, and eventually plotted to take the company and its resources to fulfill the Tech Men's true goals.

Young Justice. Aqualad/Kaldur, Black Manta's second in command is really a Fake Defector trying to get closer to the Light and their new partner. The show doesn't shy away from the moral dilemmas the mole has to face to maintain cover.

Real Life

Infamous Soviet Agent Kim Philby ended up as the head of MI6's anti-Soviet branch, Section IX, for quite some time before he was suspected of being The Mole and moved to a different position. He was well aware of the irony of this, and commented on the farcical nature of his position.

Admiral Wilhelm Canaris who was actually head of the Abwehr while also being part of the German Resistance. He was caught after the July Plot and was executed a few weeks before the war ended.

Alfred Redl was the most devastating spy Austria-Hungary ever had, giving Tsarist Russia virtually every scrap of data he could get his hands on to the point where by the time he was found out and forced to commit suicide, over a year of preparation did not even start to repair the damage by the time World War I started. Redl's role? Director of Austro-Hungarian intelligence!

Though he was retired when he was found out. Interestingly, he was only found out because he had been so good at his role as a spy master for the Habsburgs: his reforms to the intelligence service had made the counter-intelligence branch quite effective at its job.

Mark Felt, the associate director of the FBI, was put in charge of searching for Deep Throat, the source leaking information on the Watergate scandal to Bob Woodward and Carl Bernstein of The Washington Post. In 2005, he revealed that he was in fact Deep Throat himself after years of having been suspected as the primary or sole source for Deep Throat's revelations.

Israeli spy Eli Cohen, using the alias "Kamel Amin Thaabet", became Chief Advisor to the Syrian Minister of Defense and was third in line to succeed as President of Syria before he was caught and executed in 1965.

None other than Adolf Hitler, who was sent by the German military to infiltrate what would become the Nazi Party when it had less than 60 members. Nice Job Breaking It, Hero! doesn't even begin to describe it.

Yevno Azef, head of the Socialist Revolutionary Party's Combat Organisation in pre-revolutionary Russia, was also a double agent in the employ of the Okhrana. He got the top job by selling out his predecessor, who was arrested and sentenced to death (but escaped by hiding in a barrel of cabbages).

During The Vietnam War, Phạm Ngọc Thảo, a communist agent in South Vietnam managed to climb the ranks as high up as Colonel. When the South Vietnamese government tried to move the rural population into strategical hamlets to cut off Viet Cong guerrillas from their support base, Thảo was put in charge of the project. With this power, he accelerated the building of strategical hamlets to unsustainable speed. On one hand, this upset the peasants for disrupting their livelihood and leaving hamlets underfunded and insecure due to widespread corruption, thus gaining more support to the Viet Cong while giving the government false optimism with big numbers. Thảo was eventually caught and executed, but not for being a spy; rather, the President thought he was an ambitious general plotting a coup.

During his tenure as President of the Screen Actors Guild, Ronald Reagan was a secret FBI informant who got many of his colleagues blacklisted for alleged or proven Communist sympathies.

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